Re: [AMBER] generating parameters for methane

From: David A Case <>
Date: Sat, 20 Jun 2020 07:39:48 -0400

On Sat, Jun 20, 2020, angad sharma wrote:

>till here it is okay for one unit of methane but i put 0.1M methane in the
>a box ,and do the following commands then i face the given error.
>source leaprc.gaff
>loadamberparams meth.frcmod
>loadoff meth.lib
>a = loadpdb meth.pdb
>check a
>saveamberparm a a.prmtop a.inpcrd

Is the "meth.pdb" file used here the same as you used for antechamber?
Does it have just one methane molecule? (Confused because you mentioned
"0.1M" above.)

>then i get this error
>> check a
>Checking 'a'....
>ERROR: The unperturbed charge of the unit: -0.082000 is not integral.
>WARNING: The unperturbed charge of the unit: -0.082000 is not zero.
>Checking parameters for unit 'a'.
>Checking for bond parameters.
>Checking for angle parameters.
>check: Errors: 1 Warnings: 1

This is not really an error, although it is odd. Look at the charges in
your meth.mol2 or meth.lib file: do they add up to zero? You may need
to manually adjust the charges. But a deviation of 0.082 is really
large, so we need more information, as requested above.


AMBER mailing list
Received on Sat Jun 20 2020 - 05:00:03 PDT
Custom Search